BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472653.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 17,772,664 number of mapped reads = 17,629,567 (99.19%) number of supplementary alignments = 111,119 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,838,077 number of mapped paired reads (second in pair) = 8,791,490 number of mapped paired reads (both in pair) = 17,529,618 number of mapped paired reads (singletons) = 99,949 number of mapped bases = 1,737,572,353 bp number of sequenced bases = 1,737,360,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,335,082 duplication rate = 49.61% >>>>>>> Insert size mean insert size = 24,218.5532 std insert size = 1,528,208.6349 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 54.7662 >>>>>>> ACTG content number of A's = 479,283,848 bp (27.59%) number of C's = 391,701,067 bp (22.55%) number of T's = 480,107,702 bp (27.63%) number of G's = 385,935,214 bp (22.21%) number of N's = 332,584 bp (0.02%) GC percentage = 44.76% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 10,637,721 number of insertions = 118,122 mapped reads with insertion percentage = 0.66% number of deletions = 93,804 mapped reads with deletion percentage = 0.52% homopolymer indels = 44.49% >>>>>>> Coverage mean coverageData = 0.5613X std coverageData = 26.1844X There is a 3.44% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 212460712 0.8523979244168062 45.03670944273456 chr2 243199373 147399146 0.6060835773618545 25.30062540830512 chr3 198022430 174017107 0.8787747276912015 35.04534269008347 chr4 191154276 35231368 0.18430855295122983 7.970441987839789 chr5 180915260 62009139 0.34275239689565157 15.058396184163964 chr6 171115067 143612829 0.8392763508078456 30.438091686540368 chr7 159138663 105651623 0.6638966358539785 30.02790786365951 chr8 146364022 107275525 0.7329364384370362 27.47676737025554 chr9 141213431 112442290 0.7962577582298103 24.641855637291012 chr10 135534747 25550832 0.1885186829617943 10.155660040949869 chr11 135006516 39807044 0.29485276103266006 11.437441966206022 chr12 133851895 44951635 0.3358311438175754 12.97560431021908 chr13 115169878 64909551 0.563598330806602 26.628251787433236 chr14 107349540 26609165 0.24787404771366509 10.792974761243425 chr15 102531392 20087295 0.19591360858535892 14.710870166357914 chr16 90354753 94290773 1.0435618478200035 34.742522241700605 chr17 81195210 56973925 0.701690715499104 20.43397045687878 chr18 78077248 2528083 0.032379253428604454 1.2737358862538404 chr19 59128983 50590912 0.8556026069313588 37.612127197949576 chr20 63025520 89089708 1.4135497493713658 55.16558850474576 chr21 48129895 11099546 0.23061645989462473 16.261664152334227 chr22 51304566 25630796 0.4995811873742388 17.734693404513706 chrMT 16571 5996 0.3618369440588981 0.6929224729524873 chrX 155270560 82558269 0.5317058752154948 17.472363781287456 chrY 59373566 2789084 0.04697518084057811 4.042484647895422